Author: tlinnet
Date: Wed Aug 27 11:49:21 2014
New Revision: 25331
URL: http://svn.gna.org/viewcvs/relax?rev=25331&view=rev
Log:
Modified profiling script to calculate timings.
The timings for C-code are:
Simplex, with constraints = 2.192
Simplex, without constraints = 0.216
BFGS, without constraints = 0.079
Newton, without constraints = 0.031
This is pretty pretty fast.
To this profiling script, I would also now add some verification on
calculations.
Profile, with constraints, C code, Simplex
Wed Aug 27 11:45:16 2014
/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpvJSNrB
724946 function calls (723444 primitive calls) in 2.192 seconds
Ordered by: cumulative time
List reduced from 307 to 1 due to restriction <1>
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 2.192 2.192
profiling_relax_fit.py:314(verify)
Verify, without constraints, C code, Simplex
Wed Aug 27 11:45:16 2014
/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmphJ9GV3
76042 function calls (74654 primitive calls) in 0.216 seconds
Ordered by: cumulative time
List reduced from 132 to 1 due to restriction <1>
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.216 0.216
profiling_relax_fit.py:314(verify)
Verify, without constraints, C code BFGS
Wed Aug 27 11:45:16 2014
/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmp78MZjS
25618 function calls (24230 primitive calls) in 0.079 seconds
Ordered by: cumulative time
List reduced from 153 to 1 due to restriction <1>
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.079 0.079
profiling_relax_fit.py:314(verify)
Verify, without constraints, C code Newton
Wed Aug 27 11:45:16 2014
/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmp2IPgFC
14572 function calls (13184 primitive calls) in 0.031 seconds
Ordered by: cumulative time
List reduced from 169 to 1 due to restriction <1>
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.031 0.031
profiling_relax_fit.py:314(verify)
Verify, with constraints, Python, Simplex
Wed Aug 27 11:45:20 2014
/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpQUUY4L
808444 function calls (806942 primitive calls) in 3.108 seconds
Ordered by: cumulative time
List reduced from 141 to 1 due to restriction <1>
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 3.108 3.108
profiling_relax_fit.py:353(verify_pyt)
Verify, without constraints, Python, Simplex
Wed Aug 27 11:45:20 2014
/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmp3nFBTq
87492 function calls (86104 primitive calls) in 0.320 seconds
Ordered by: cumulative time
List reduced from 131 to 1 due to restriction <1>
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.320 0.320
profiling_relax_fit.py:353(verify_pyt)
Verify, without constraints, Python Scipy
Wed Aug 27 11:45:20 2014
/var/folders/ww/1jkhkh315x57jglgxnr9g24w0000gp/T/tmpo1HoWn
6600 function calls (5212 primitive calls) in 0.020 seconds
Ordered by: cumulative time
List reduced from 137 to 1 due to restriction <1>
ncalls tottime percall cumtime percall filename:lineno(function)
1 0.000 0.000 0.020 0.020
profiling_relax_fit.py:388(verify_sci)
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
Modified:
trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py
Modified:
trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py?rev=25331&r1=25330&r2=25331&view=diff
==============================================================================
---
trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py
(original)
+++
trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py
Wed Aug 27 11:49:21 2014
@@ -57,7 +57,8 @@
# relax module imports.
from status import Status; status = Status()
from specific_analyses.relax_disp.estimate_r2eff import minimise_leastsq, Exp
-from target_functions.relax_fit import setup, func, dfunc, d2func,
back_calc_I
+from specific_analyses.relax_fit.optimisation import func_wrapper,
dfunc_wrapper, d2func_wrapper
+from target_functions.relax_fit import setup
from target_functions.chi2 import chi2_rankN
## Set the min_algor.
@@ -114,7 +115,7 @@
print("C_cT=%1.1e C_cF=%1.1e P_cT=%1.1e P_cF=%1.1e" %
(chi_v_cT-chi_v_cT, chi_v_cF-chi_v_cT, chi_v_pyt_cT-chi_v_cT,
chi_v_pyt_cF-chi_v_cT) )
# Do verification for Python code, and difference between minfx and
Scipy optimisation without constraints.
- if True:
+ if False:
# Calculate with Python code.
# Calculate without contraints.
v_pyt_cF_chi2_list = array(verify_pyt(constraints=False))
@@ -132,10 +133,12 @@
print("P_cF=%1.1e Sci_cF=%1.1e" % (chi_v_pyt_cF-chi_v_pyt_cF,
chi_v_pyt_cF-chi_v_sci_cF) )
# Do profiling.
-
if True:
- #################
- print("Verify, with constraints, C code")
+ print("\n################################# Profiling
#################################")
+
+
+ #################
+ print("#####################\nProfile, with constraints, C code,
Simplex \n#####################")
constraints = True
# Print statistics.
@@ -148,9 +151,8 @@
print_report(filename=filename, verbose=verbose)
- if True:
- #################
- print("Verify, without constraints, C code")
+ #################
+ print("#####################\n Verify, without constraints, C code,
Simplex \n#####################")
constraints = False
# Print statistics.
@@ -163,9 +165,8 @@
print_report(filename=filename, verbose=verbose)
- if True:
- #################
- print("Verify, without constraints, C code BFGS")
+ #################
+ print("#####################\n Verify, without constraints, C code
BFGS \n#####################")
constraints = False
# Print statistics.
@@ -178,9 +179,24 @@
print_report(filename=filename, verbose=verbose)
- if False:
- #################
- print("Verify, with constraints, Python")
+
+ #################
+ print("#####################\n Verify, without constraints, C code
Newton \n#####################")
+ constraints = False
+
+ # Print statistics.
+ verbose = True
+
+ # Calc for verify with constraints.
+ filename = tempfile.NamedTemporaryFile(delete=False).name
+ # Profile for a single spin.
+ cProfile.run('verify(min_algor="Newton",
constraints=%s)'%(constraints), filename)
+
+ print_report(filename=filename, verbose=verbose)
+
+
+ #################
+ print("#####################\n Verify, with constraints, Python,
Simplex \n#####################")
constraints = True
# Print statistics.
@@ -193,9 +209,8 @@
print_report(filename=filename, verbose=verbose)
- if False:
- #################
- print("Verify, without constraints, Python")
+ #################
+ print("#####################\n Verify, without constraints, Python,
Simplex \n#####################")
constraints = False
# Print statistics.
@@ -208,9 +223,8 @@
print_report(filename=filename, verbose=verbose)
- if True:
- #################
- print("Verify, without constraints, Python Scipy")
+ #################
+ print("#####################\n Verify, without constraints, Python
Scipy \n#####################")
# Print statistics.
verbose = True
@@ -316,6 +330,11 @@
E.set_settings_minfx(min_algor=min_algor, constraints=constraints)
+ # Define func.
+ func = func_wrapper
+ dfunc = dfunc_wrapper
+ d2func = d2func_wrapper
+
# Initialise the function to minimise.
scaling_list = [1.0, 1.0]
setup(num_params=len(x0), num_times=len(E.times), values=E.values,
sd=E.errors, relax_times=E.times, scaling_matrix=scaling_list)
@@ -353,6 +372,7 @@
# Define func.
func = E.func_exp
dfunc = E.func_exp_grad
+ d2func = None
results = generic_minimise(func=func, dfunc=dfunc, d2func=d2func,
args=(), x0=x0, min_algor=E.min_algor, min_options=E.min_options,
func_tol=E.func_tol, grad_tol=E.grad_tol, maxiter=E.max_iterations, A=E.A,
b=E.b, full_output=True, print_flag=E.verbosity)
r25331 - /trunk/test_suite/shared_data/curve_fitting/profiling/profiling_relax_fit.py